Profile

Prof Albe van der Merwe

Associate Professor
Department
Biochemistry, Genetics and Microbiology
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Member of:

Research Profiles

My Students

Primary Supervisor

Johan Griesel

Michal Slupski

Bio

My scientific interest is in population genetics and phylogeography of plant pathogenic fungi and the plants they infect. I use Chrysoporthe austroafricana, C. deuterocubensis and C. cubensis as fungal models to test hypotheses about how plant pathogens evolved, how they spread from one area to another, and what the future impact of anthropogenic phenomena such as climate change might be.

I am investigating the population genetics of these fungi from various countries and continents, using molecular markers to infer statistics describing populations' outcrossing abilities, recombination rates and linkage disequilibrium, and gene flow. I also have a special interest in gene trees and coalescent theory as applied to these fungi.

An exciting era is about to dawn on forest tree and pathogen genetics, and I am proud and priviledged to be a part of it. As Prof. Michio Kaku said, we are moving from scientific discovery to scientific mastery, and I believe that the current efforts by FABI and its programmes will play a crucial role in realizing this dream.

Teaching

Current Courses:

(2014-) GTS354: Genome Evolution & Phylogenetics

Past Courses:

(2014-2015) GTS367: Advanced Population Genetics
(2010-2013) GTS353: Population Genetics & The Evolution of Quantitative Traits
(2010-2013) GTS366: Plant Genetics & Biotechnology

Information for prospective students

Any prospective post-graduate student is welcome to apply for post-graduate studies with me. However, please take note of the following requirements so that you don't waste your own time.

All students

Preference will be given to South African students, but that does not preclude foreigners from applying to study with me. In fact, I always have one or more foreign students in my programme.

BSc Honours

Prospective Honours students should apply to the Department of Biochemistry, Genetics and Microbiology through the University of Pretoria's online application system. The Department then places Honours students with supervisors.

Prospective MSc students

Send me and email and attach your Curriculum Vitae, email addresses and telephone numbers of two referees (one of which is your previous supervisor), your Honours project report (SA residents), or a poster or presentation that you have delivered. If you have already published a paper in an ISI rated journal, attach that too. Important: You must be able to fund your own subsistence either through a bursary (attach evidence) or personal funds.

Prospective PhD students

Send me an email and attach your Curriculum Vitae, email addresses and telephone numbers of two referees (one of which is your previous supervisor), your MSc dissertation, and an ISI-rated article where you were the first author. Important: You must be able to fund your own subsistence either through a bursary (attach evidence) or personal funds.

Git repositories

Debian Science User Repository

Much of the software I use needs manual compilation, resulting in installation errors or misconfigurations. Thus, I decided to package some of this software for Debian(-based) systems, and I call it the Debian Science User Repository. If you have an amd64 computer running Debian, you can peek at the DSUR and see if there is anything you can use.

Diaporthales genomes sequenced in my lab

Although links are provided to other sources where genomes can be obtained, the Git repository should be considered the most current.

Species	Isolate	Repository	Publications
Chrysoporthe austroafricana MAT-2	CMW 2113	GitLab NCBI	Announcement
Chrysoporthe austroafricana MAT-1	CMW 6102	GitLab
Chrysoporthe cubensis	CMW 10028	GitLab NCBI	Announcement
Chrysoporthe deuterocubensis	CMW 8650	GitLab NCBI	Announcement

Other public Diaporthales genomes

These genomes were sequenced by other groups.

Species	Isolate	Repository
Cryphonectria parasitica	EP 155	GitLab NCBI

My Journal Articles

Export to RIS

Publication
Swalarsk-Parry BS, De Vos L, Fru FF, Santana QC, van der Nest MA, Wingfield BD, Wingfield MJ, Herron DA, Ramaswe JB, Dewing C, Sayari M, van der Merwe NA, van Wyk S, Lane FA, Wilson AM, Adegeye OO, Soal NC, Price J-L, Steenkamp ET. (2024) *Wide variation in aggressiveness and growth in South African Fusarium circinatum* isolates with geographical origin as the primary determinant*. Southern Forests: a Journal of Forest Science* 10.2989/20702620.2024.2363749
Aylward J, Wilson AM, Visagie CM, Spraker J, Barnes I, Buitendag C, Ceriani C, Del Mar Angel L, du Plessis D, Fuchs T, Gasser K, Krämer D, Li W, Munsamy K, Piso A, Price J-L, Sonnekus B, Thomas C, van der Nest A, van Dijk A, van Heerden A, van Vuuren N, Yilmaz N, Duong TA, van der Merwe NA, Wingfield MJ, Wingfield BD. (2024) IMA Genome – F19: A genome assembly and annotation guide to empower mycologists, including annotated draft genome sequences of Ceratocystis pirilliformis, Diaporthe australafricana, Fusarium ophioides, Paecilomyces lecythidis, and Sporothrix stenoceras. IMA Fungus 15(1):12. 10.1186/s43008-024-00142-z
Miyambo TM, Backer R, Engelbrecht J, Joubert F, van der Merwe NA, van den Berg N. (2022) The Identification and Characterization of Endopolygalacturonases in a South African Isolate of Phytophthora cinnamomi. Microorganisms 10(1061) 10.3390/microorganisms10051061
van Wyk S, Wingfield B, De Vos L, van der Merwe A, Steenkamp E. (2021) Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota. Frontiers in Microbiology 11(Article 622368):1-17. 10.3389/fmicb.2020.622368
Van der Nest M, Hlongwane N, Hadebe K, Chan W, Van der Merwe N, De Vos L, Greyling B, Kooverjee B, Soma P, Dzomba E, Bradfield M, Muchadeyi F. (2021) Breed ancestry, divergence, admixture, and selection patterns of the Simbra crossbreed. Frontiers in Genetics 11:1796. 10.3389/fgene.2020.608650
Roux J, Nkuekan GK, Marincowitz S, van der Merwe NA, Uchida J, Wingfield MJ, Chen SF. (2020) *Chryphonectriaceae associated with rust-infected Syzigium jambos* in Hawaii.*. MycoKeys* 76:49-79. 10.3897/mycokeys.76.58406
Oliveira MES, van der Merwe NA, Wingfield MJ, Wingfield BD, Soares TPF, Kanzi AM, Ferreira MA. (2020) Chrysoporthe puriensis sp. nov. from Tibouchina spp. in Brazil: an emerging threat to Eucalyptus. Australasian Plant Pathology 10.1007/s13313-020-00745-1
van Wyk S, Wingfield BD, De Vos L, van der Merwe NA, Santana QC, Steenkamp ET. (2019) Repeat-Induced Point Mutations Drive Divergence between Fusarium circinatum and Its Close Relatives. Pathogens 8(298):1-21. 10.3390/pathogens8040298
van Wyk S, Harrison CH, Wingfield BD, De Vos L, van der Merwe NA, Steenkamp ET. (2019) The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations. PeerJ 7:e7447. 10.7717/peerj.7447
Kanzi AM, Steenkamp ET, Van der Merwe NA, Wingfield BD. (2019) *The mating system of the Eucalyptus* canker pathogen Chrysoporthe austroafricana and closely related species*. Fungal Genetics and Biology* 123:41-52. 10.1016/j.fgb.2018.12.001
Baron S, Van der Merwe NA, Maritz-Olivier C. (2018) The genetic relationship between R. microplus and R. decoloratus ticks in South Africa and their population structure. Molecular Phylogenetics and Evolution 129:60-69. 10.1016/j.ympev.2018.08.003
Fourie G, van der Merwe NA, Wingfield BD, Bogale M, Wingfield MJ, Steenkamp ET. (2018) Mitochondrial introgression and interspecies recombination in the Fusarium fujikuroi species complex. IMA Fungus 9(1):37-48. 10.5598/imafungus.2018.09.01.04
Van Wyk S, Wingfield BD, De Vos L, Santana QC, Van der Merwe N, Steenkamp ET. (2018) Multiple independent origins for a subtelomeric locus associated with growth rate in Fusarium circinatum. IMA Fungus 9(1):27-36. 10.5598/imafungus.2018.09.01.03
Sungirai M, Baron S, Van der Merwe NA, Moyo DZ, De Clercq P, Maritz-Olivier C, Madder M. (2018) *Population structure and genetic diversity of Rhipicephalus microplus* in Zimbabwe*. Acta Tropica* 180:42-46. 10.1016/j.actatropica.2018.01.003
Coetzee MPA, Musasira NY, Roux J, Roets F, van der Merwe NA, Wingfield MJ. (2018) Armillaria root rot spreading into a natural woody ecosystem in South Africa. Plant Pathology 10.1111/ppa.12804
Wingfield BD, Berger DK, Steenkamp ET, Lim H-J, Duong TA, Bluhm BH, De Beer ZW, De Vos L, Fourie G, Naidoo K, Olivier NA, Lin Y, Van der Peer Y, Joubert F, Crampton BG, Swart V, Soal N, Tatham C, Van der Nest MA, Van der Merwe NA, Van Wyk S, Wilken PM, Wingfield MJ. (2017) IMA Genome-F 8 Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips. IMA Fungus 8 (2):385‑396. 10.5598/imafungus.2017.08.02.10
Masumba EA, Kapinga F, Mkamilo G, Salum K, Kulembeka H, Rounsley S, Bredeson JV, Lyons JB, Rokhsar DS, Kanju E, Katari MS, Myburg AA, van der Merwe NA, Ferguson ME. (2017) QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert. Theoretical and Applied Genetics 130(10):2069-2090. 10.1007/s00122-017-2943-z
Zwart L, Berger DK, Moleleki LN, Van der Merwe NA, Myburg AA, Naidoo S. (2017) Evidence for salicylic acid signalling and histological changes in the defence response of Eucalyptus grandis to Chrysoporthe austroafricana. Scientific Reports 7:45402. 10.1038/srep45402
Kanzi AM, Wingfield BD, Steenkamp ET, Naidoo S, Van der Merwe NA. (2016) *Intron derived size polymorphism in the mitochondrial genomes of closely related Chrysoporthe* species*. PLOS ONE* 11(6):e0156104. 10.1371/journal.pone.0156104
Chen SF, van der Merwe NA, Wingfield MJ, Roux J. (2016) *Population structure of Holocryphia capensis* (Cryphonectriaceae) from Metrosideros angustifolia and its pathogenicity to Eucalyptus species*. Australasian Plant Pathology* 45(2):201-207. 10.1007/s13313-016-0399-2
Robbertse L, Baron S, van der Merwe NA, Madder M, Stoltsz WH, Maritz-Olivier C. (2016) *Genetic diversity, acaricide resistance status and evolutionary potential of a Rhipicephalus microplus* population from a disease-controlled cattle farming area in South Africa*. Ticks and Tick-borne Diseases* 10.1016/j.ttbdis.2016.02.018
Wingfield BD, Barnes I, De Beer ZW, De Vos L, Duong TA, Kanzi AM, Naidoo K, Nguyen HDT, Santana QC, Sayari M, Seifert KA, Steenkamp ET, Trollip C, Van der Merwe N, Van der Nest MA, Wilken PM, Wingfield MJ. (2015) Draft genome sequences of Ceratocystis eucalypticola, Chrysoporthe cubensis, C. deuterocubensis, Davidsoniella virescens, Fusarium temperatum, Graphilbum fragrans, Penicillium nordicum, and Thielaviopsis musarum. IMA Fungus 6(2):493-506. 10.5598/imafungus.2015.06.02.13
Baron S, Van der Merwe NA, Madder M, Maritz-Olivier C. (2015) SNP analysis infers that recombination is involved in the evolution of Amitraz resistance in Rhipicephalus microplus. PLoS ONE 10(7):e0131341. 10.1371/journal.pone.0131341
Wingfield BD, Ades PK, Al-Naemi FA, Beirn LA, Bihon W, Crouch JA, De Beer ZW, De Vos L, Duong TA, Fields CJ, Fourie G, Kanzi AM, Malapi-Wight M, Pethybridge SJ, Radwan O, Rendon G, Slippers B, Santana QC, Steenkamp ET, Taylor PWJ, Vaghefi N, Van der Merwe NA, Veltri D, Wingfield MJ. (2015) IMA Genome-F 4. Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata. IMA Fungus 6(1):233-248. 10.5598/imafungus.2015.06.01.15
Crous PW, Wingfield MJ, Guarro J, Hernandez-Restrepo M, Sutton DA, Acharya K, Barber PA, Boekhout T, Dimitrov RA, Duenas M, Dutta AK, Gene J, Gouliamova DE, Groenewald M, Lombard L, Morozova OV, Sarkar J, Smith MTh, Stchigel AM, Wiederhold NP, Alexandrova AV, Antelmi I, Armengol J, Barnes I, Cano-Lira JF, Castaneda Ruiz RF, Contu M, Courtecuisse PrR, Da Silveira AL, Decock CA, De Goes A, Edathodu J, Ercole E, Firmino AC, Fourie A, Fournier J, Furtado EL, Geering ADW, Gershenzon J, Giraldo A, Gramaje D, Hammerbacher A, He X-L, Haryadi D, Khemmuk W, Kovalenko AE, Krawczynski R, Laich F, Lechat C, Lopes UP, Madrid H, Malysheva EF, Marin-Felix Y, Martin MP, Mostert L, Nigro F, Pereira OL, Picillo B, Pinho DB, Popov ES, Rodas Pelaez CA, Rooney-Latham S, Sandoval-Denis M, Shivas RG, Silva V, Stoilova-Disheva MM, Telleria MT, Ullah C, Unsicker SB, Van der Merwe NA, Vizzini A, Wagner H-G, Wong PTW, Wood AR, Groenewald JZ. (2015) Fungal Planet description sheets: 320–370. Persoonia 34:167-266. 10.3767/003158515X688433
Woudenberg JC, van der Merwe NA, Jurjević Z, Groenewald JZ, Crous PW. (2015) *Diversity and movement of indoor Alternaria alternata* across the mainland USA*. Fungal Genetics and Biology* 81:62-72. 10.1016/j.fgb.2015.05.003
Lombard L, van der Merwe NA, Groenewald JZ, Crous PW. (2015) Generic concepts in Nectriaceae. Studies in Mycology 80:189-245. 10.1016/j.simyco.2014.12.002
De Vos L, Steenkamp ET, Martin SH, Santana QC, Fourie G, Van der Merwe NA, Wingfield MJ, Wingfied BD. (2014) *Genome-wide macrosynteny among Fusarium* species in the Gibberella fujikuroi complex revealed by amplified fragment length polymorphisms*. PLoS ONE* 9(12):e114682. 10.1371/journal.pone.0114682
Lombard L, Van der Merwe NA, Groenewald JZ, Crous PW. (2014) *Lineages in Nectriaceae: re-evaluating the generic status of Ilyonectria* and allied genera*. Phytopathologia Mediterranea* 53(3):515-532. 10.14601/Phytopathol_Mediterr-14976
De Vos L, van der Merwe NA, Wingfield MJ, Myburg AA, Wingfield BD. (2013) Transmission ratio distortion in an interspecific cross between Fusarium circinatum and Fusarium subglutinans. Genes and Genomics 35:1-7. 10.1007/s13258-013-0066-8
Fourie G, van der Merwe NA, Wingfield BD, Bogale M, Tudzynski B, Wingfield MJ, Steenkamp ET. (2013) *Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium* species in the Gibberella fujikuroi complex*. BMC Genomics* 14:605. 10.1186/1471-2164-14-605
Louw E, van der Merwe NA, Neitz AWH, Maritz-Olivier C. (2013) Evolution of the tissue factor pathway inhibitor-like Kunitz domain-containing protein family in Rhipicephalus microplus. International Journal for Parasitology 43:81-94. 10.1016/j.ijpara.2012.11.006
Van der Merwe NA, Steenkamp ET, Rodas C, Wingfield BD, Wingfield MJ. (2013) *Host switching between native and non-native trees in a population of the canker pathogen Chrysoporthe cubensis* from Colombia*. Plant Pathology* 62:642-648. 10.1111/j.1365-3059.2012.02657.x
Wingfield BD, Steenkamp ET, Santana QC, Coetzee MPA, Bam S, Barnes I, Beukes CW, Chane W-Y, de Vos L, Fourie G, Friend M, Gordon TR, Herron DA, Holt C, Korf I, Kvas M, Martin SH, Mlonyeni XO, Naidoo K, Phasha MM, Postma A, Reva O, Roos H, Simpson M, Slinski S, Slippers B, Sutherland R, van der Merwe NA, van der Nest MA, Venter SNV, Wilken PM, Yandell M, Zipfel R, Wingfield MJ. (2012) First fungal genome sequence from Africa: a preliminary analysis. South African Journal of Science 108:104-122. 10.4102/sajs.v108i1/2.537
De Vos L, van der Nest MA, van der Merwe NA, Myburg AA, Wingfield MJ, Wingfield BD. (2011) Genetic analysis of growth, morphology and pathogenicity in the F1 progeny of an interspecific cross between Fusarium circinatum and Fusarium subglutinans. Fungal Biology 115(9):902-908. 10.1016/j.funbio.2011.07.003
van der Merwe NA, Gryzenhout M, Steenkamp ET, Wingfield BD, Wingfield MJ. (2010) Multigene phylogenetic and population differentiation data confirm the existence of a cryptic species within Chrysoporthe cubensis. Fungal Biology 114(11-12):966-979. 10.1016/j.funbio.2010.09.007
Hunter GC, Van Der Merwe NA, Burgess TI, Carnegie AJ, Wingfield BD, Crous PW, Wingfield MJ. (2008) Global movement and population biology of Mycosphaerella nubilosa infecting leaves of cold-tolerant Eucalyptus globulus and E. nitens. Plant Pathology 57(2):235-242. 10.1111/j.1365-3059.2007.01756.x
Van Wyk M, Van Der Merwe NA, Roux J, Wingfield BD, Kamgan GN, Wingfield MJ. (2006) *Population genetic analyses suggest that the Eucalyptus* fungal pathogen Ceratocystis fimbriata has been introduced into South Africa*. South African Journal of Science* 102(5-6):259-263.
Gryzenhout M, Myburg H, Van Der Merwe NA, Wingfield BD, Wingfield MJ. (2004) **Chrysoporthe, a new genus to accommodate Cryphonectria cubensis*. Studies in Mycology* 50:119-141.
Van Der Merwe NA, Wingfield BD, Wingfield MJ. (2003) *Primers for the amplification of sequence-characterized loci in Cryphonectria cubensis* populations*. Molecular Ecology Notes* 3(4):494-497. 10.1046/j.1471-8286.2003.00508.x
Van der Merwe NA, Myburg H, Wingfield BD, Rodas C, Wingfield MJ. (2001) *Identification of Cryphonectria cubensis* from Colombia based on rDNA sequence data*. South African Journal of Science* 97(7-8):295-296.